Panax pseudoginseng growers, in pursuit of maximum yields and economic benefits, blindly increase irrigation water and excessive application of pesticides and chemical fertilizers, resulting in the accumulation of soil nutrients year by year, nutrient leaching loss, soil environmental quality and yield saponin content decline in the outstanding problems, the study provides technical support for the efficient use and management of Panax pseudoginseng water and fertilizers, and has important practical significance for high yield and quality planting of Panax pseudoginseng. In this paper, three irrigation levels of W1 (5.00 mm), W2 (10.00 mm), and W3 (15.00 mm) were set for Panax pseudoginseng at the root growth stage, seedling stage, flowering stage, and fruiting stage, and four organic fertilizer application levels of F1 (48.00 kg.hm− 2), F2 (72.00 kg.hm− 2), F3 (96.00 kg.hm− 2) and F4 (120.00 kg.hm− 2) were used for the study from 2018 to 2020 in Luxi County, Honghe Prefecture, Yunnan Province. F2 (72.00 kg.hm− 2), F3 (96.00 kg.hm− 2), and F4 (120.00 kg.hm− 2) were tested in the field with the optimal strategy. The results showed that the soil microbial biomass carbon and nitrogen content, soil urease, sucrase, acid phosphatase, and catalase activities differed significantly (p < 0.05) at different fertility periods with the same irrigation rate and organic fertilizer application, and the soil microbiomes carbon and nitrogen content and enzyme activities had the characteristics of increasing first and then decreasing with the extension of fertility period and increasing with the increase of irrigation rate and fertilizer application. Soil acid phosphatase and catalase were the main microbial quantity carbon and nitrogen control factors, urease was the main microbial quantity carbon control factor and sucrase was the main microbial quantity nitrogen control factor, and there was no correlation between soil water content and microbial quantity carbon and nitrogen (p > 0.05). The differences in yield, saponin content, water use efficiency, and fertilizer bias productivity of Panax pseudoginseng with different irrigation and organic fertilizer were highly significant (p < 0.01), yield increased and then decreased with increasing irrigation and fertilizer application, water use efficiency decreased with increasing irrigation and increased with increasing fertilizer application, fertilizer bias productivity decreased with increasing fertilizer application and was highly significant (p < 0.01) with irrigation, saponin The saponin content increased and then decreased with the increase of irrigation water, and decreased and then increased with the increase of fertilizer application. Panax pseudoginseng yield, saponin content, water use efficiency, and fertilizer utilization were the highest in W2F3 and W2F4 treatments and the lowest in CK treatment. The overall evaluation was that the optimal irrigation amount was 10 mm and the fertilizer application rate was 120 kg.hm− 2 at the root growth stage of Panax pseudoginseng, and the optimal irrigation amount was 15 mm and the fertilizer application rate was 120 kg.hm− 2 at the seedling, flowering and fruiting stages, and both W2F3 and W2F4 treatments improved the carbon and nitrogen content and enzyme activity of soil microorganisms, which were conducive to improving yield quality and water and fertilizer productivity.